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Cell Biosci. 2020 Mar 10;10:33. doi: 10.1186/s13578-020-00399-y. eCollection 2020.

Alternative splicing signatures in preimplantation embryo development.

Tian GG1, Li J1,2, Wu J1,3,4.

Author information

1Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China.
3Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China.
Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, NingxiaMedicalUniversity, Yinchuan, 750004 China.
Shanghai Key Laboratory of Reproductive Medicine, Shanghai, 200025 China.



Preimplantation embryo development is a highly ordered sequence of processes and it requires a precise temporal and spatial control of gene expression. Alternative splicing (AS) is a crucial process that changes the genomic instructions into functional proteins, playing a critical role in the regulation of gene expression. Therefore, studies of AS can significantly improve our understanding of transcription and splicing events in preimplantation embryo development.


To study signatures of AS in embryo development, we firstly identified the critical stage for gene transcription during the preimplantation embryo development. By analyzing single cells RNA-seq (scRNA-seq) data, we found that the two-cell stage is a critical stage for gene transcription in preimplantation embryo development. Further study showed that AS was widespread in preimplantation embryo development, especially at the two-cell stage. In combination with high-throughput chromosome conformation (Hi-C) data, we demonstrated that AS genes were highly enriched in TAD boundaries, while they had no relationship with the A/B compartment and TAD.


Our results provide new insight into the relationship among AS, gene transcription and chromatin structure in preimplantation embryo development.

Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests.

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